The Obama administration’s political operation failed to clear the field in Pennsylvania for Specter, whose three-decade Senate career was ended by Sestak — a candidate many in Washington felt can’t win statewide in the general election.

Halter’s candidacy was backed by Democratic-allied groups such as MoveOn.org and the AFL-CIO, who were angered by Lincoln’s perceived rejection of the Obama administration’s agenda.

His union allies said Tuesday’s result should send a “clear message.”

"Working families all over the state of Arkansas have sent a clear message: They will not stand up for those who fail to stand for them. What Sen. Lincoln learned tonight and what elected leaders all around this country should note is that the days of 'business as usual' are over," SEIU President Mary Kay Henry said in a statement.

AFL-CIO President Richard Trumka vowed to press on and defeat Lincoln in the June 8 runoff.

“From the minute the polls closed tonight, we began our renewed efforts to elect Bill Halter to the Senate in the runoff election,” he said in a statement.

It was a harsh loss for the National Republican Congressional Committee, which spent close to $1 million supporting Burns’s campaign. Democrats hyped expectations for the GOP’s win in recent days, which will only add salt to the committee’s wounds.

But the Senate primaries in Arkansas and Pennsylvania show there is discontent among voters with the party’s leadership. The Democratic establishment went firmly for Specter in Pennsylvania. Obama helped him raise money, appeared in his TV commercials and lent his voice to a robo-call. The Democratic Senatorial Campaign Committee spent money on Specter’s behalf in the weeks leading up to the election.

T.J. Rooney, chairman of the state party, campaigned with the senator in the final days, while Gov. Ed Rendell and Rep. Chaka Fattah (D-Pa.) rallied supporters in and around Philadelphia to get out in support of Specter.

In Arkansas, Obama recorded a robo-call for Lincoln and directed Organizing for America to help her get out the vote.

The Republican rank and file sent a similar message of discontent in Kentucky, opting to nominate Paul ahead of the GOP establishment-backed Trey Grayson.